If I understand you correctly this has nothing to do with the audio interface you only need to program a modifier on every cdj that cdj 1 controls deck a or c; cdj 2 b or d. Everything else is bound permanently in your example to the decks.

If we talk about the Traktor scratch audio 6 you only need the 2 inputs for the 2 ttables - in your example they were connected to c and d, and the other stuff is just a question if midi mapping like I said and has nothing to do with the interface. And you will of course also be able to have an output to the PA and one separate for your headphones like it should be.